Tidy-up batch: docs, schema, configs, single trivial correctness fix#1849
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- README: mark Preseq optional and add a RustQC bullet - nextflow_schema.json: strip TODOs from kallisto_quant_fraglen[_sd] descriptions, clarify base-pair units, declare default false for skip_dupradar/qualimap/rseqc/biotype_qc/deseq2_qc, note RustQC supersession - workflows/rnaseq/main.nf: bitwise & -> logical && in three skip_qc guards - modules/local/deseq2_qc: replace input-dependent stub shell loop with deterministic touch calls - conf/modules/featurecounts.config: drop duplicate CUSTOM_MULTIQCCUSTOMBIOTYPE block (kept in multiqc_custom_biotype.config) - conf/modules/align_star.config: merge two adjacent withName blocks for the same selector - bin/fastq_dir_to_samplesheet.py: remove unmaintained script (superseded by nf-core/fetchngs) - ro-crate-metadata.json: refresh embedded README description
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- README: prefix the RustQC bullet with "experimental" and the "trial on pilot data first" caveat already used in the schema - nextflow_schema.json: drop "RustQC supersedes this tool" from the four QC skip_* descriptions; replace with a shorter "no effect under --use_rustqc (experimental)" note - ro-crate-metadata.json: refresh embedded README description
The module test (modules/local/deseq2_qc/tests/main.nf.test) snapshots process.out.size_factors, which captures one per-sample *.size_factors.RData file derived from the data columns of the input counts. Replacing the loop with fixed sample1/sample2 touches changed the stub output and broke the snapshot on docker and docker-arm64 shard 2. Restore the original `for i in ...` loop and add a short comment explaining why the stub mirrors the live-run behaviour. Drop the "deterministic deseq2_qc stub" claim from the #1849 CHANGELOG entry.
…-1845 # Conflicts: # CHANGELOG.md
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Thanks @vagkaratzas ! |
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Summary
Bundles tidy-ups from #1845 — no behaviour, runtime, or output changes.
skip_preseq = trueby default) and add a bullet pointing at RustQC as an experimental single-pass alternative to RSeQC/Qualimap/dupRadar/Preseq/SAMtools-stats (matches the existing schema framing).nextflow_schema.json: dropTODO: ...text that was leaking into the rendered help forkallisto_quant_fraglenandkallisto_quant_fraglen_sd; clarify the values are in base pairs.nextflow_schema.json: explicitly declare"default": falseforskip_dupradar,skip_qualimap,skip_rseqc,skip_biotype_qc,skip_deseq2_qc(matchingnextflow.config), and note that the four QC-tool flags have no effect under--use_rustqc(experimental).workflows/rnaseq/main.nf: change three guard conditions from bitwise&to logical&&for consistency with the rest of the file (no behaviour change since operands are always truthy/falsy).conf/modules/featurecounts.config: delete the duplicatewithName: 'CUSTOM_MULTIQCCUSTOMBIOTYPE'block (the same block inconf/modules/multiqc_custom_biotype.configis the authoritative one and wins by inclusion order).conf/modules/align_star.config: merge two adjacentwithNameblocks that target the same selector (one setext.args, the otherpublishDir) into a single block.bin/fastq_dir_to_samplesheet.py: not referenced from any.nf, last functional change in 2023; CHANGELOG already directs users to nf-core/fetchngs for samplesheet generation.modules/local/deseq2_qc/main.nf: kept the stub's input-drivenfor i in \head $counts -n 1 | cut -f3-`loop and added a short comment explaining why — the module test snapshotsprocess.out.size_factors` and asserts one per-sample file per data column of the input counts, so the stub must mirror live-run output. (Tidy-up batch: docs, schema, configs, single trivial correctness fix #1845 sub-item 5 was originally to replace the loop with fixed touches, but per the issue's own guidance "if any one of them turns out to be more involved than expected, drop it from this PR" the deeper change is left for a follow-up.)ro-crate-metadata.jsonis updated bynf-core pipelines lint --fixto keep the embedded README description in sync.Closes #1845.
Test plan
nf-core pipelines lintpasses (0 failed, 600 passed; only pre-existing warnings remain)